Synthetic molecular systems

Miniature machines captivate human imagination. From a flight of a bee to a beating of a flagellum, the ability of tiny creatures to perform seemingly impossible tasks inspire us with awe. While scaling up in size human technology is relatively straightforward, scaling down the systems and mechanisms without loosing functionality, ultimately to the molecular scale, remains a major challenge. The dominance of stochastic forces over gravity and inertia, surface effects over body forces, and granularity of conventional materials render application of macroscopic engineering principles at the nanoscale obsolete. While human efforts to engineer and build nanomachines have so far produced rather modest results, biology provides outstanding examples of what can be accomplished. This research thrust focuses on the development of synthetic analogs to landmark biomolecular machines such as autonomous nanoscale walkers, selective nanochannels gated by external stimuli, and membrane-bound energy conversion systems.

Membrane protein channels involved in cellular signal transductions are fascinating biological sensors with high selectivity and efficiency. Recently, DNA origami nanostructures emerged as highly customizable mimetics of biological membrane channels. A typical DNA membrane channel is assembled from several DNA double helices arranged into a polygon pattern, with the central cavity forming the transmembrane pore. To facilitate insertion of the DNA channel into a lipid bilayer membrane, the DNA helices are chemically modified to carry hydrophobic anchors. Until now, most of the DNA channels featured four or six DNA helices arranged in a square or a hexagon, with the inner channel diameter varying between 1 and 2.5 nm. Using all-atom Molecular Dynamics (MD) simulation, we characterized the biophysical properties of the DNA membrane channels with atomic precision. We further engineered DNA membrane channels that span one order of magnitude in diameter and three orders of magnitude in conductance and molecular weight, covering the entire range of the protein membrane channels.